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Detailed information for vg0323811167:

Variant ID: vg0323811167 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 23811167
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCCCTAGTAAAACTTTTTTAAATTTAATAAAGTCTATAGGAAAACACAATAGTATTTTTAATACAAAACAAACATATTATGAAAACATACTCAATGTTA[G/T]
ATTTAATTAACATATTATGAAAGTGACTTATTATAATATAAAACAGAAGGGTTTCCTAGTGCGTCCTTTGAGAAAAGTTGCTTGAGAATTGAAAATGGTA

Reverse complement sequence

TACCATTTTCAATTCTCAAGCAACTTTTCTCAAAGGACGCACTAGGAAACCCTTCTGTTTTATATTATAATAAGTCACTTTCATAATATGTTAATTAAAT[C/A]
TAACATTGAGTATGTTTTCATAATATGTTTGTTTTGTATTAAAAATACTATTGTGTTTTCCTATAGACTTTATTAAATTTAAAAAAGTTTTACTAGGGGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.00%	25.60%	0.42%	0.00%	NA
All Indica	2759	98.90%	1.10%	0.00%	0.00%	NA
All Japonica	1512	27.80%	71.00%	1.19%	0.00%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	97.70%	2.30%	0.00%	0.00%	NA
Temperate Japonica	767	33.80%	64.10%	2.09%	0.00%	NA
Tropical Japonica	504	14.90%	84.90%	0.20%	0.00%	NA
Japonica Intermediate	241	36.10%	63.50%	0.41%	0.00%	NA
VI/Aromatic	96	26.00%	74.00%	0.00%	0.00%	NA
Intermediate	90	65.60%	32.20%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0323811167	G -> T	LOC_Os03g42750.1	upstream_gene_variant ; 2818.0bp to feature; MODIFIER	silent_mutation	Average:57.412; most accessible tissue: Zhenshan97 root, score: 81.974	N	N	N	N
vg0323811167	G -> T	LOC_Os03g42760.1	upstream_gene_variant ; 1398.0bp to feature; MODIFIER	silent_mutation	Average:57.412; most accessible tissue: Zhenshan97 root, score: 81.974	N	N	N	N
vg0323811167	G -> T	LOC_Os03g42750.2	upstream_gene_variant ; 2818.0bp to feature; MODIFIER	silent_mutation	Average:57.412; most accessible tissue: Zhenshan97 root, score: 81.974	N	N	N	N
vg0323811167	G -> T	LOC_Os03g42750-LOC_Os03g42760	intergenic_region ; MODIFIER	silent_mutation	Average:57.412; most accessible tissue: Zhenshan97 root, score: 81.974	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0323811167	4.04E-06	4.04E-06	mr1061	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251